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Generate info from my snps

well finally I got my snps with added gen...of course a lot of extra information like.... 

chr1    14815   0   C   T   0.00012928  0   AB=0    ABP=0   AC=0    AF=0    AN=2    AO=3    CIGAR=1X    DP=14   DPB=14  DPRA=0  EPP=3.73412 EPPR=7.94546    GTI=0   LEN=1   MEANALT=1   MQM=6   MQMR=8.27273    NS=1    NUMALT=1    ODDS=10.4802    PAIRED=0    PAIREDR=0   PAO=0   PQA=0   PQR=0   PRO=0   QA=77   QR=242  RO=11   RPL=1   RPP=3.73412 RPPR=4.78696    RPR=2   RUN=1   SAF=3   SAP=9.52472 SAR=0   SRF=5   SRP=3.20771 SRR=6   TYPE=snp    technology.IONTORRENTIon=1  GENE=WASH7P GT:DP:DPR:RO:QR:AO:QA:GL    0/0:14:14   3:11:242:3:77:0 -2.55149    -5.77448

Now what I want is to compare for example in a family having the xls from each individual, which snps they share(same position, same base) and make my own tables, as well to be able to generate a report with the info of the genes which are in common (just as sample). I dont know if is better work directly with vcf files or my snps calls xls table.

Any ideas how I can start looking?

Im newbeee!!!

Thanks!!!!!

snp
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updated by GenoMax GenoMax • written by cristina_sabiers cristina_sabiers

If you want to know the intersect between two vcf file "shared between two samples for examples" you can use bedtools ,
for comparing you can also use SnpSift Concordance also it contains a lot of features that could help you also can use VCFtools

for example

vcf-compare

Compares positions in two or more VCF files and outputs the numbers of positions contained in one but not the other files; two but not the other files, etc, which comes handy when generating Venn diagrams. The script also computes numbers such as nonreference discordance rates (including multiallelic sites), compares actual sequence (useful when comparing indels), etc.

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written by Medhat Medhat

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